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This week in DIYbio!

March 26, 2009

titojankowski

Microfluidics, a competition for free sequencing, an abundance of ideas for cheap lab equipment both second-hand and DIY, and thoughtful discussions on the current state of public perception and the future of regulation have made for quite an interesting week in DIYbio.

Projects

Bryan Bishop and others experiment with Sharpies and glass slides for making DIY microfluidics.

Why not sequence a genome? Sandra Porter suggests the idea and and Jason Bobe shares a writeup on a likely partner for this, Cofactor Genomics. No sooner does Jason suggest raising funds, and pledges $100 to kick-start the idea, than Tito Jankowski mentions the fact that Cofactor is running a contest for a free ~700Mb sequencing project for education. Follow along on the “Why not sequence a genome?” thread.

Equipment

Lots of people ask about the best way to get started with a DIY lab setup for doing amateur biology. It turns out that now is a great time to shop for your lab on eBay! Aaron Hicks shares his experience on in the “DIY Lab Setup” discussion thread.

Dan Heidel posts a review of a nice (and affordable) $100 pipetter set.

Cheap CCDs might enable building spectrophotometers and using dynamic light-scattering to probe the sizes of molecules in a solution in the “DIY biophysical setups?” thread.

Regulation and perception

An article from GenomeWeb gets us thinking about the perception by the public and the larger scientific establishment. A prolific discussion ensues.

Bryan Bishop brings up a new report out of U. Virginia “New Life, Old Bottles: Regulating First Generation Products of Synthetic Biology“, with video.

Extract DNA from Strawberries

March 20, 2009

titojankowski

Yummy strawberries

Yummy strawberries have lots of DNA

Syndicated from thetech.org “Do-it-yourself Strawberry DNA”

Strawberries, bacteria, humans—all living things have genes, and all of these genes are made of DNA. That’s why scientists can take a gene from one living thing and put it into another. For example, they can put human genes into bacteria to make new medicines.

How do scientists take DNA out of a living thing? It’s not that hard—there are lots of ways to do it! You can follow the directions in the video below to get DNA out of a strawberry. Or you can follow the steps after that. Either way you’ll have strawberry DNA at the end!

What you need:

  • measuring cup
  • measuring spoons
  • rubbing alcohol
  • 1/2 teaspoon salt
  • 1/3 cup water
  • 1 tablespoon Dawn dishwashing detergent
  • glass or small bowl
  • cheesecloth
  • funnel
  • tall drinking glass
  • 3 strawberries (green tops removed)
  • reclosable plastic sandwich bags
  • test tube or small glass jar (like the kind spices come in)
  • bamboo skewer or kabob sticks  (find them at the grocery store)

What to do:

  1. Chill the rubbing alcohol in the freezer. (You’ll need it later.)
  2. Mix the salt, water, and Dawn detergent in a glass or small bowl. Set the mixture aside. This is your extraction liquid.
  3. Line the funnel with the cheesecloth, and put the funnel’s tube into the glass.
  4. Put the strawberries in the plastic bag and push out all the extra air. Seal it tightly.
  5. With your fingers, squeeze and smash the strawberry mixture for 2 minutes.
  6. Add 3 tablespoons of the extraction liquid you made in Step 2 to the strawberries in the bag. Push out all the extra air and reseal the bag.
  7. Squeeze the strawberry mixture with your fingers for 1 minute.
  8. Pour the strawberry mixture from the bag into the funnel. Let it drip into the glass until there is no liquid left in the funnel.
  9. Throw away the cheesecloth and the strawberry pulp inside. Pour the contents of the glass into the test tube or small glass jar so it is 1/4 full.
  10. Tilt the test tube or jar and very slowly pour the cold rubbing alcohol down the side. The alcohol should form a layer on top of the strawberry liquid. (Don’t let the alcohol and strawberry liquid mix. The DNA collects between the two layers!)
  11. Dip the bamboo skewer into the test tube where the alcohol and strawberry layers meet. Pull up the skewer. The whitish, stringy stuff is DNA containing strawberry genes!

You can try these steps to purify DNA from lots of other living things. Grab some oatmeal or kiwis from the kitchen and try it again! Which foods give you the most DNA?

Here is a link to troubleshooting tips and FAQ list from the “Extract DNA from Anything Living” experiment: 20 Most Frequently Asked Questions

This Week in DIYbio – Match 15, 2009 Edition

March 15, 2009

Jason Bobe

Howdy DIYbioers! Thanks for stopping by. Here are a few highlights from the past week:

Discussions and happenings this week

DIYbio in the Big Apple – The NYC DIYbio group had a meetup on March 9th, and has started a blog and YouTube channel.

Basics of gel electrophoresis – Dan Heidel gives an excellent and readable rundown of the basics of gel electrophoresis.

Biology forums – Ellen Jorgensen and Bryan Bishop shared a set of forums where anyone can ask technical questions about their work. Ellen recommended the (very active) forums from Biotechniques magazine, and Bryan shared a comprehensive list of other related forums.

Citizen science for climate and plants – Cory Tobin shared a call for citizen scientists from the Nature Climate Feedback blog, which may be of interest to some DIYbio scientists, along with a podcast from the US Geological Survey about the program.

Do your biology in space – Jonathan Cline mentioned CubeSat, a platform for 10 cm^3, 1 kg satellite projects, and included links to design specifications as well as information about a developer meetup in April.

Projects for the Amateur Scientist – Jason Morrison shared a link to a PDF of C.L. Stong’s Projects for the Amateur Scientist (1960), which contains several very approachable amateur biology protocols.

Get your DIYbio any way you like it!

The DIYbio mailing list is a great resource and full of vibrant discussion, but sometimes it’s a bit much to handle. Luckily, you can edit your subscription settings and elect to receive only daily digests, or turn off email entirely and catch up on discussion at your own pace by reading the DIYbio mailing list online.

As an alternative, you can subscribe to the very low-traffic DIYbio Announce list, which has less than five messages per week.

Lastly, for those of you on Twitter, come follow DIYbio on Twitter! We’ll tweet interesting information, letting you know about big DIYbio publications, news, and events.

So, until next week, keep experimenting, keep safe, and keep sharing your science!
— Jason M.

DIYbio in 4 minutes – O’Reilly Ignite Boston 5

March 5, 2009

100ideas

I gave another lightning talk about DIYbio at Ignite Boston 5 in February 09.

http://vimeo.com/moogaloop.swf?clip_id=3454392&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=00ADEF&fullscreen=1
The DIYbio Community – Presented at Ignite Boston 5 (2009) from mac cowell on Vimeo.

We founded diybio.org, a community for amateur scientists, last year in May, just in time to present at ignite boston 2008. Since then, the community has grown. In this talk, I spend 5 minutes giving a lighting overview of the community and the current hot projects members are working on: new, cheap, diy-hardware, distributed science experiments (think flashmobs for science), a biohacking coworking space, and some molecular biology experiments (including making genetically engineered fluorescent yogurt, a melamine biosensor, and a biological counter).